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Build all atoms of a protein given its CA coordinates

Method
First all atoms of the backbone are built, using a library of (overlapping) fragments of length 4 taken from the PDB database. This will inevitably cause a slight -but acceptable- displacement of the CA atoms, ususally on the order of 0.5-0.8 Angstrom.
Then all sidechain atoms are constructed, using our Mean-Field Optimisation in-house technique (Koehl and Delarue, J. Mol. Biol., 1994, 239:249-275).

This is intended to be used for the transition state coordinates, obtained from the "Trajectory" Option.

Your email adress: (Recommended, for notification)


Job title: (Only alphanumerical characters)


PDB file name (CA only) Ex: 1OMP_ca.pdb


Strength of the constraint on CA positions

Number of cycles for energy minimisation



Input data formats

  • The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).

  • The coordinate files should be in PDB format, with only a single structure (no multiple models). Only CA atoms are accepted as this stage; the limit is 1000 residues. The program does not know how to handle breaks in the chain due to several subunits.
    If there are several subunits, each one should be submitted separately for reconstruction.





  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:18 November 07, 2008.